R/report_VPA.R

In SAMtool: Stock Assessment Methods Toolkit

summary_VPA <- function(Assessment) {
  assign_Assessment_slots(Assessment)

  if (conv) current_status <- c(F_FMSY[length(F_FMSY)], SSB_SSBMSY[length(SSB_SSBMSY)], SSB_SSB0[length(SSB_SSB0)])
  else current_status <- rep(NA, 3)
  current_status <- data.frame(Value = current_status)
  rownames(current_status) <- c("F/FMSY", "SSB/SSBMSY", "SSB/SSB0")

  Value <- c(h, info$data$M[1], min(info$ages), max(info$ages), info$LH$Linf, info$LH$K, info$LH$t0,
             info$LH$a * info$LH$Linf ^ info$LH$b, info$LH$A50, info$LH$A95)
  Description = c("Stock-recruit steepness", "Natural mortality", "Minimum age (minus-group)", "Maximum age (plus-group)", "Asymptotic length",
                  "Growth coefficient", "Age at length-zero", "Asymptotic weight", "Age of 50% maturity", "Age of 95% maturity")
  rownam <- c("h", "M", "minage", "maxage", "Linf", "K", "t0", "Winf", "A50", "A95")
  input_parameters <- data.frame(Value = Value, Description = Description, stringsAsFactors = FALSE)
  rownames(input_parameters) <- rownam
  if (!info$fix_h) input_parameters <- input_parameters[-1, ]

  if (conv) Value <- c(VB0, SSB0, MSY, FMSY, VBMSY, SSBMSY, SSBMSY/SSB0)
  else Value <- rep(NA, 7)

  Description <- c("Unfished vulnerable biomass",
                  "Unfished spawning stock biomass (SSB)", "Maximum sustainable yield (MSY)", "Fishing mortality at MSY",
                  "Vulnerable biomass at MSY", "SSB at MSY", "Spawning depletion at MSY")
  derived <- data.frame(Value = Value, Description = Description, stringsAsFactors = FALSE)
  rownames(derived) <- c("VB0", "SSB0", "MSY", "UMSY", "VBMSY", "SSBMSY", "SSBMSY/SSB0")

  model_estimates <- sdreport_int(SD)

  output <- list(model = "Virtual Population Analysis (VPA)",
                 current_status = current_status, input_parameters = input_parameters,
                 derived_quantities = derived, model_estimates = model_estimates,
                 log_likelihood = matrix(NLL, ncol = 1, dimnames = list(names(NLL), "Neg.LL")))
  return(output)
}
class(VPA) <- "Assessment"

rmd_VPA <- function(Assessment, ...) {
  ss <- rmd_summary("Virtual Population Analysis (VPA)")

  # Life History
  LH_section <- c(rmd_LAA("info$ages", header = "## Life History\n"), rmd_WAA("info$ages"), rmd_LW(),
                  rmd_mat("info$ages", "info$LH$mat", 
                          fig.cap = "Maturity at age. Length-based maturity parameters were converted to the corresponding ages."))

  # Data section
  data_section <- c(rmd_data_timeseries("Catch", header = "## Data\n"), 
                    rmd_data_timeseries("Index", is_matrix = is.matrix(Assessment@Obs_Index), nsets = ncol(Assessment@Obs_Index)),
                    rmd_data_age_comps("bubble", ages = "info$ages"),
                    rmd_data_age_comps("annual", ages = "info$ages", annual_yscale = "\"raw\"", annual_ylab = "\"Catch-at-age\""))

  # Assessment
  #### Pars and Fit
  assess_fit <- c("## Assessment {.tabset}\n### Estimates and Model Fit\n",
                  rmd_sel("info$ages", fig.cap = "Estimated terminal-year selectivity at age."),
                  rmd_assess_fit_series(nsets = ncol(Assessment@Index)),
                  rmd_fit_age_comps("annual", ages = "info$ages", match = TRUE))

  #### Time Series
  ts_output <- c(rmd_F(header = "### Time Series Output\n", fig.cap = "apical fishing mortality"), rmd_F_FMSY(),
                 rmd_sel_annual("info$ages"), rmd_sel_persp("info$ages"),
                 #rmd_U(fig.cap = "harvest rate (ratio of catch and vulnerable biomass)"),
                 #rmd_U_UMSY(fig.cap = "U/UMSY, where UMSY = MSY/VBMSY"),
                 rmd_SSB(), rmd_SSB_SSBMSY(), rmd_SSB_SSB0(),
                 rmd_Kobe("SSB_SSBMSY", "F_FMSY", xlab = "expression(SSB/SSB[MSY])", ylab = "expression(F/F[MSY])"),
                 #rmd_Kobe("SSB_SSBMSY", "U_UMSY", xlab = "expression(SSB/SSB[MSY])", ylab = "expression(U/U[MSY])"),
                 rmd_R(), rmd_N(), rmd_N_at_age(ages = "info$ages"), rmd_C_at_age(ages = "info$ages"), 
                 rmd_C_mean_age(ages = "info$ages"))

  # Productivity
  SR_calc <- c("SSB_SR <- SSB[1:(length(SSB) - min(info$ages))]",
               "R_SR <- R_pred(SSB_SR, TMB_report$h, TMB_report$R0, TMB_report$E0, info$SR)",
               "Rest <- R[(min(info$ages)+1):length(SSB)]")
  productivity <- c(rmd_SR(ylab = paste0("Recruitment (age ", min(Assessment@info$ages), ")"),
                           header = "### Productivity\n\n\n", conv_check = TRUE,
                           SR_calc = SR_calc),
                    rmd_SR(ylab = paste0("Recruitment (age ", min(Assessment@info$ages), ")"),
                           fig.cap = "Stock-recruit relationship (trajectory plot).", trajectory = TRUE, conv_check = TRUE),
                    rmd_yield_F("VPA"), rmd_yield_depletion("VPA"), rmd_sp(depletion = FALSE), rmd_YPR(), rmd_SPR())

  return(c(ss, LH_section, data_section, assess_fit, ts_output, productivity))
}


plot_yield_VPA <- function(data, report, fmsy, msy, xaxis = c("F", "Biomass", "Depletion")) {
  plot_yield_SCA(data = data, report = report, fmsy = fmsy, msy = msy, xaxis = xaxis)
}

profile_likelihood_VPA <- function(Assessment, ...) {
  dots <- list(...)
  if (!"Fterm" %in% names(dots)) stop("Sequence of Fterm was not found. See help file.")
  Fterm <- dots$Fterm

  params <- Assessment@info$params
  map <- Assessment@obj$env$map
  map$log_Fterm <- factor(NA)

  profile_fn <- function(i, Assessment, params, map) {
    params$log_Fterm <- log(Fterm[i])
    obj2 <- MakeADFun(data = Assessment@info$data, parameters = params, map = map, DLL = "SAMtool", silent = TRUE)
    opt2 <- optimize_TMB_model(obj2, Assessment@info$control, do_sd = FALSE)[[1]]
    if (!is.character(opt2)) nll <- opt2$objective else nll <- NA_real_
    return(nll)
  }
  nll <- vapply(1:length(Fterm), profile_fn, numeric(1), Assessment = Assessment, params = params, map = map) - Assessment@opt$objective
  profile_grid <- data.frame(Fterm = Fterm, nll = nll)

  pars <- "Fterm"
  MLE <- Assessment@SD$value["Fterm"]

  output <- new("prof", Model = Assessment@Model, Name = Assessment@Name, Par = pars, MLE = MLE, grid = profile_grid)
  return(output)
}


retrospective_VPA <- function(Assessment, nyr) {
  assign_Assessment_slots(Assessment)
  n_y <- info$data$n_y
  Year <- c(info$Year, max(info$Year) + 1)

  # Array dimension: Retroyr, Year, ts
  # ts includes: F, SSB, R, VB
  retro_ts <- array(NA, dim = c(nyr+1, n_y + 1, 4))
  TS_var <- c("F", "SSB", "R", "VB")
  dimnames(retro_ts) <- list(Peel = 0:nyr, Year = Year, Var = TS_var)

  retro_est <- array(NA, dim = c(nyr+1, dim(summary(SD))))
  dimnames(retro_est) <- list(Peel = 0:nyr, Var = rownames(summary(SD)), Value = c("Estimate", "Std. Error"))

  lapply_fn <- function(i, info, obj) {
    n_y_ret <- n_y - i
    info$data$n_y <- n_y_ret
    info$data$I_hist <- info$data$I_hist[1:n_y_ret, , drop = FALSE]
    info$data$CAA_hist <- info$data$CAA_hist[1:n_y_ret, ]

    obj2 <- MakeADFun(data = info$data, parameters = info$params, map = obj$env$map, DLL = "SAMtool", silent = TRUE)
    mod <- optimize_TMB_model(obj2, info$control)
    opt2 <- mod[[1]]
    SD <- mod[[2]]

    if (!is.character(opt2)) {
      report <- obj2$report(obj2$env$last.par.best) %>% VPA_posthoc(info)

      #Z_mat <- t(report$F) + info$data$M
      #VB_mid <- t(report$N[-ncol(report$N), ]) * (1 - exp(-Z_mat))/Z_mat
      #U <- c(colSums(t(report$CAApred) * info$data$weight)/colSums(VB_mid), rep(NA, i + 1))
      
      FMort <- c(report$F, rep(NA, i + 1))
      SSB <- c(report$E, rep(NA, i))
      R <- c(report$N[, 1], rep(NA, i))
      VB <- c(report$VB, rep(NA, i))

      retro_ts[i+1, , ] <<- cbind(FMort, SSB, R, VB)
      retro_est[i+1, , ] <<- summary(SD)

      return(SD$pdHess)
    }
    return(FALSE)
  }

  conv <- vapply(0:nyr, lapply_fn, logical(1), info = info, obj = obj)
  if (any(!conv)) warning("Peels that did not converge: ", paste0(which(!conv) - 1, collapse = " "))

  retro <- new("retro", Model = Assessment@Model, Name = Assessment@Name, TS_var = TS_var, TS = retro_ts,
               Est_var = dimnames(retro_est)[[2]], Est = retro_est)
  attr(retro, "TS_lab") <- c("Apical fishing mortality", "Spawning biomass", "Recruitment", "Vulnerable biomass")

  return(retro)
}